Biomedical Applications of Raman Scattering
R. Michael Gendreau in Spectroscopy in the Biomedical Sciences, 1986
As an example of the procedure, in an α-helix there are 18 peptide bonds per 5 turns of helix while interchain hydrogen bonds are found between each pair of every third neighbor. It is verifiable from group theory that the frequencies of the Raman-active modes occur = 0, 100, and 200°, respectively (corresponding in group theoretical language to the A1, E1, and E2 modes of vibration). For homopolypeptides of α-helical structure it is found that these three modes occur with very similar frequencies. This arises because the magnitudes of D and D′ are similar but of opposite sign. The α-helical Amide I frequencies all appear at 1650 ± 5 cm−1. For the antiparallel pleated sheet, a unit cell contains four peptide groups, two each from two adjacent chains. The values of δ and δ′ permitted are each 0 or 180°.
Exploring the Folding and Aggregation Mechanisms of Amyloid-Forming Peptides by Computer Simulations
Gilles Grateau, Robert A. Kyle, Martha Skinner in Amyloid and Amyloidosis, 2004
Analysis of the lowest-energy structures generated by all ART simulations shows several interesting features. Firstly, although the antiparallel beta-sheet arrangement is the most stable structure for the dimer and the trimer, in agreement with the NMR solid state of the fibril Aβ16-22 at neutral pH (4), several hydrogen-bond patterns with similar free energies exist (see the results on the dimer in Figure 1). This indicates that full structural order in the fibrils requires larger aggregates. Secondly, a parallel beta-sheet structure with low free energy is possible for the dimer, and mixed antiparallel-parallel organizations are also possible for the trimer. This result is significant because it helps clarify the dependency of beta-sheet registries on pH conditions (8). Thirdly, the folding pathways do not require obligatory α-helical intermediates. This finding indicates that destabilization of α-helical inter-mediates is unlikely to abolish oligomerization of full-length Aβ peptides. Finally, our simulations also emphasize the crucial role of the reptation move of one strand of the beta-sheet with respect to the others during the assembly process. Again, this is consistent with recent isotope-edited infrared spectroscopy analysis on the prion peptide spanning residues 109-122 (9).
Interleukin-6 Receptor
Andrzej Mackiewicz, Irving Kushner, Heinz Baumann in Acute Phase Proteins, 2020
Molecular cloning of the cDNAs coding for the receptors of IL-2 (β and γ subunit), IL-3, IL-4, IL-5, IL-6 (80- and 130-kDa subunits), IL-7, IL-9, growth hormone, prolactin, erythropoietin, granulocyte colony-stimulating factor, granulocyte/macrophage colony-stimulating factor (both subunits), leukemia inhibitory factor, and the comparison of the respective amino acid sequences led to the recognition of an absolute conservation of four cysteine residues and a Trp-Ser-X-Trp-Ser (WSXWS) motif. However, the overall sequence homology between the cytokine receptors mentioned is only about 20%.46,47 In addition, Bazan proposes that seven consensus β-strands form an antiparallel β-sandwich with a topology analogous to an immunoglobulin constant domain. The receptors listed above form a new family of cytokine receptors also designated as a hematopoietic or hemopoietin receptor superfamily (Figure 16).
Human antimicrobial peptides in autoimmunity
Published in Autoimmunity, 2020
Ekaterina S. Umnyakova, Maria S. Zharkova, Mikhail N. Berlov, Olga V. Shamova, Vladimir N. Kokryakov
In the early 60s of the 20th century small cationic polypeptides with low molecular weight and a high antimicrobial activity were investigated in guinea pig and rabbit neutrophil granules [8–10]. Later related peptides were revealed in human neutrophils, and such peptides were named defensins [11]. Defensins are a group of multifunctional cationic peptides with common properties:A high content of basic amino acid residues (arginine and lysine).Prevalence of antiparallel β-sheets in their secondary structure.Six conservative cysteines that form 3 intramolecular disulphide bonds, stabilising secondary and tertiary structures.Amphipathic spatial structure of molecules.Compact defensin structure provides sustainability to proteases activity.
A novel CRYGC E128* mutation underlying an autosomal dominant nuclear cataract in a south Indian kindred
Published in Ophthalmic Genetics, 2020
Dinesh Kumar Kandaswamy, K. Vasantha, Jochen Graw, Sathiyaveedu Thyagarajan Santhiya
Lens crystallins constitute about 90% of the total soluble protein content of the lens, and 35% of the total lens mass. They are composed of two broad classes: α and βγ. βγ-crystallins are enriched in the central portion of the lens the embryonic nuclear region, from where the lens grows, is rich in γ-crystallins. Crystallins are the earliest to be expressed in tune with the lens morphogenesis. The β and γ-crystallins share a common feature of antiparallel β sheets in the protein, which is referred to as “Greek key motif.” The γ-crystallin proteins are tightly folded into two domains with no free loops. Each domain consists of two Greek-key motifs, folded as hairpin that provides stability between two β-sheets (12). These folds and domain interactions contribute high thermodynamic stability to the lens proteins.
Fibrinogen alpha amyloidosis: insights from proteomics
Published in Expert Review of Proteomics, 2019
Amyloidoses are a group of diseases that result from the systemic or localized deposition of amyloid fibrils in the extra-cellular spaces of tissues causing organ dysfunction and potentially death. These diseases can affect any organ and are often underdiagnosed. Amyloid fibrils are insoluble protein aggregates that form when a protein becomes misfolded. There are 36 biochemically diverse proteins that are accepted to cause amyloidosis, but the common feature of these proteins is the propensity to form beta-pleated sheets under appropriate conditions (Table 1) [20]. The beta-pleated sheets align in an antiparallel fashion and through hydrogen bond interactions form long protofilaments. Protofilaments interact via their side chains to form fibrils [21]. These rigid fibrils resist proteolysis in the affected tissues and organs [22,23].
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